Spin-phonon coupling plays an important role in single-molecule magnets and molecular qubits. However, there have been few detailed studies of its nature. Here, we show for the first time distinct couplings of g phonons of CoII(acac)2(H2O)2 (acac = acetylacetonate) and its deuterated analogs with zero-field-split, excited magnetic/spin levels (Kramers doublet (KD)) of the S = 3/2 electronic ground state. The couplings are observed as avoided crossings in magnetic-field-dependent Raman spectra with coupling constants of 1-2 cm-1. Far-IR spectra reveal the magnetic-dipole-allowed, inter-KD transition, shifting to higher energy with increasing field. Density functional theory calculations are used to rationalize energies and symmetries of the phonons. A vibronic coupling model, supported by electronic structure calculations, is proposed to rationalize the behavior of the coupled Raman peaks. This work spectroscopically reveals and quantitates the spin-phonon couplings in typical transition metal complexes and sheds light on the origin of the spin-phonon entanglement.